fnirt --in=struct_brain --aff=my_affine_transf.mat --cout=my_nonlinear_transf --ref=MNI152_T1_2mm_brain --config=T1_2_MNI152_2mm --iout=struct_MNI
--in输入：struct_brain
--aff仿射矩阵：my_affine_transf.mat
--cout：带有场系数（field coefficients）的输出矩阵(应该是变换矩阵)
--ref参考图像(目标图像)：MNI152_T1_2mm_brain
--config：指定命令行参数的配置文件的名称
--iout：输出图像名称 struct_MNI
Usage:
fnirt --ref=<some template> --in=<some image>
fnirt --ref=<some template> --in=<some image> --infwhm=8,4,2 --subsamp=4,2,1 --warpres=8,8,8
Compulsory arguments (You MUST set one or more of):
--ref name of reference image
--in name of input image
Optional arguments (You may optionally specify one or more of):
--aff name of file containing affine transform
--inwarp name of file containing initial non-linear warps
--intin name of file/files containing initial intensity mapping
--cout name of output file with field coefficients
--iout name of output image
--fout name of output file with field
--jout name of file for writing out the Jacobian of the field (for diagnostic or VBM purposes)
--refout name of file for writing out intensity modulated --ref (for diagnostic purposes)
--intout name of files for writing information pertaining to intensity mapping
--logout Name of log-file
--config Name of config file specifying command line arguments
--refmask name of file with mask in reference space
--inmask name of file with mask in input image space
--applyrefmask Use specified refmask if set, default 1 (true)
--applyinmask Use specified inmask if set, default 1 (true)
--imprefm If =1, use implicit masking based on value in --ref image. Default =1
--impinm If =1, use implicit masking based on value in --in image, Default =1
--imprefval Value to mask out in --ref image. Default =0.0
--impinval Value to mask out in --in image. Default =0.0
--minmet non-linear minimisation method [lm | scg] (Levenberg-Marquardt or Scaled Conjugate Gradient)
--miter Max # of non-linear iterations, default 5,5,5,5
--subsamp sub-sampling scheme, default 4,2,1,1
--warpres (approximate) resolution (in mm) of warp basis in x-, y- and z-direction, default 10,10,10
--splineorder Order of spline, 2->Quadratic spline, 3->Cubic spline. Default=3
--infwhm FWHM (in mm) of gaussian smoothing kernel for input volume, default 6,4,2,2
--reffwhm FWHM (in mm) of gaussian smoothing kernel for ref volume, default 4,2,0,0
--regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
--lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documentation.
--ssqlambda If set (=1), lambda is weighted by current ssq, default 1
--jacrange Allowed range of Jacobian determinants, default 0.01,100.0
--refderiv If =1, ref image is used to calculate derivatives. Default =0
--intmod Model for intensity-mapping [none global_linear global_non_linear local_linear global_non_linear_with_bias local_non_linear]
--intorder Order of polynomial for mapping intensities, default 5
--biasres Resolution (in mm) of bias-field modelling local intensities, default 50,50,50
--biaslambda Weight of regularisation for bias-field, default 10000
--estint Estimate intensity-mapping if set, default 1 (true)
--numprec Precision for representing Hessian, double or float. Default double
--interp Image interpolation model, linear or spline. Default linear
-v,--verbose Print diagnostic information while running
-h,--help display help info
